The main problem is the plotting and the fact that it just feels like the same thing over and over again. I was sat there at one point thinking "oh goody, yet another fight with lots of Agent Smiths".

I'm sure there was plenty of other stuff that I didn't enjoy, but I have only seen 2 and 3 once and it is hard to remember even what the "plots" were now. I do remember how badly they sucked though
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Remind me to change my signature to something more interesting someday